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- PDB-2x0p: CO-COMPLEX STRUCTURE OF ALCALIGIN BIOSYNTHETASE PROTEIN C (ALCC) ... -

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Basic information

Entry
Database: PDB / ID: 2x0p
TitleCO-COMPLEX STRUCTURE OF ALCALIGIN BIOSYNTHETASE PROTEIN C (ALCC) WITH ADENOSINE FROM Bordetella bronchiseptica
ComponentsALCALIGIN BIOSYNTHESIS PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / ALCALIGIN BIOSYNTHESIS / ADENYLATION / SIDEROPHORES / IRON ACQUISITION
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / AlcC / Alcaligin biosynthesis protein
Similarity search - Component
Biological speciesBORDETELLA BRONCHISEPTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchmelz, S. / Challis, G.L. / Naismith, J.H.
CitationJournal: To be Published
Title: Co-Complex Structure of Alcaligin Biosynthetase Protein C (Alcc) with Adenosine from Bordetella Bronchiseptica
Authors: Schmelz, S. / Challis, G.L. / Naismith, J.H.
History
DepositionDec 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6996
Polymers70,0481
Non-polymers6515
Water5,134285
1
A: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules

A: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,39912
Polymers140,0962
Non-polymers1,30310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7080 Å2
ΔGint-148 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.964, 128.948, 48.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALCALIGIN BIOSYNTHESIS PROTEIN / ALCC


Mass: 70047.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Plasmid: PET-151/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94255, UniProt: Q7W557*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 1.6 M MGSO4, 0.14 M LI2S04 AND PROTEIN SOLUTION (2.5 MG/ML ALCC, 45 MM MES PH 6.5 AND 5 MM ADENOSINE, PRE INCUBATED FOR 30 MIN ON ICE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9835
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9835 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 34630 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1 / Redundancy: 4.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.54
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X0O

2x0o


Resolution: 2.1→45.18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.711 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1789 5.2 %RANDOM
Rwork0.19625 ---
obs0.19896 32751 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---2.07 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 39 285 4918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9626507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1165576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45823.304227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5861533
X-RAY DIFFRACTIONr_chiral_restr0.0890.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023703
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22276
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23232
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.52984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25624651
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80832080
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.764.51855
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 135 -
Rwork0.266 2333 -
obs--97.98 %

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